Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Liver
Cell type
Liver
MeSH Description
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Attributes by original data submitter

Sample

ENA first public
2012-06-25
ENA last update
2018-03-08
External Id
SAMEA1464826
INSDC center alias
UNIVERSITY OF PENNSYLVANIA
INSDC center name
University of Pennsylvania, USA
INSDC first public
2012-06-25T20:05:40Z
INSDC last update
2018-03-08T15:33:19Z
INSDC status
public
StrainOrLine
Caucasian
Submitter Id
E-MTAB-805:Human-Foxa2-PM
broker name
ArrayExpress
common name
human
organism part
liver
sample name
E-MTAB-805:Human-Foxa2-PM
sex
female

Sequenced DNA Library

library_name
Hu_Liver_PM_FoxA2
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Briefly, 14-15 day old mice were injected with DEN (20 mg/kg body weight) (Sigma) to initiate tumor growth. Beginning at 28 days, mice were injected with TCPOBOP (3 mg/kg bodyweight) (Sigma) once every two weeks for a total of eight times to promote tumor growth.DEN-induced liver injury experiments were carried out as described previously (Naugler etal., 2007), except that 50 mg/kg body weight Faslodex or estrogen were intraperitoneally injected daily for seven days before DEN treatment. The human samples were not treated. Chromatin was extracted from mouse livers following the protocol described in Li et al. NSMB 2011 [PMID 21623366]. ChIP was performed on the liver chromatin samples. ChIP-DNA was prepared for sequencing with the Illumina GAII sequencer at the Functional Genomics Center at the Institute for Diabetes, Obesity and Metabolismat the University of Pennsylvania.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg38

Number of total reads
8342173
Reads aligned (%)
95.5
Duplicates removed (%)
11.0
Number of peaks
384 (qval < 1E-05)

hg19

Number of total reads
8342173
Reads aligned (%)
94.5
Duplicates removed (%)
12.3
Number of peaks
555 (qval < 1E-05)

Base call quality data from DBCLS SRA